There’s a war on. In fact, there are many of them. They’re wars waged with blueprints, long, photocopied forms and incomprehensible legal documents: the patent wars, a pencil jammed into the eye of innovation, a distraction screwing up the long-term strategies of Apple, Facebook, Google, Microsoft and many more companies besides. Software patents are fundamentally flawed, with individuals gaining commercial rights over features that should be ubiquitous, such as “slide to unlock” functionality.

Take the example of Mark Zuckerberg’s first patent. Only just awarded but brewing for years, Zuck’s masterstroke is related to – wait for it – privacy. US patent 8,225,376, “Dynamically Generating a Privacy Summary”, covers a method of displaying a user’s profile so that they are able to see what aspects are visible to other users or user groups.

Let’s pass over the glaring irony of Zuckerberg’s name appearing on such a patent. There are wider issues. The breadth of applications covered by Zuck’s original application is why it took over six years for the US Patent and Trademark Office (USPTO) to finally approve it and why Facebook had to fight so hard for that achievement.

On its own, it is trivial. It won’t protect Facebook in any meaningful way, nor is it vital to the company’s business interests. Rather, its acquisition is a personal trophy for the Facebook boss who still associates himself heavily with the hacker ethos and a conviction that he likes, knows and understands developer psychology. That he himself has not tinkered with any significant code for quite some time is irrelevant.

The patent also forms part of a wider battle front for Facebook, which has been rapidly increasing its defensive portfolio. In the wake of its recent patent settlement with Yahoo!, it has been purchasing hundreds of patents to build an arsenal, often doing deals with AOL and Microsoft. Over 500 patents have been transferred from AOL to Facebook in the past month.

It is not alone in the arms race. Twitter has also been buying up patents, like a crazed supermarket shopper grabbing canned goods before a hurricane. Microsoft already creams a healthy chunk off every Android sale, thanks to judicious use of its patent arsenal and those fights have led Google to gobble up as many patents as possible itself. Meanwhile, Apple has just grabbed a 13-year-old multitouch patent to strengthen its hand in its ongoing fight with Google and its satellite states, Samsung and HTC.

Why does all this legal wrangling matter to consumers? Because it has a material effect on software innovation and the products you can actually buy. More and more frequently, consumer technology firms are succeeding in gaining injunctions that prevent rival products from hitting the shelves. And while the big beasts can fight back, small outfits, especially in software development, are becoming highly risk adverse.

Notch, the genius behind Minecraft who has turned Mojang into a gaming powerhouse, warned this week about the damage the patent war is doing: “Trivial patents such as for software, are counterproductive (they slow down technical advancement), evil (they sacrifice baby goats to Baal) and costly (companies get tied up in pointless lawsuits). If you own a software patent, you should feel bad.”

It’s worth noting, before people start accusing Notch of supporting the “freetard” revolution, that he is not arguing for copyright infringement. In fact, he explicitly states that is not the case: “I am mostly fine with the concept of ‘selling stuff you made’, so I’m against copyright infringement… but there is no way in hell you can convince me that it’s beneficial for society to not share ideas.

“Ideas are free. They improve on old things, make them better and this results in all of society being better…”

While couched in somewhat hippyish terms, Notch has got it spot on. Developers and creators are becoming increasingly hostile toward the idea of software patents. They are clumsy coshes with which major companies assert their dominance, often prompting markets to stagnate. The only thing truly enriched by software patents are lawyers’ bank accounts.

Of course, protecting innovation while still encouraging new entrants into the market is difficult. The problem is systemic. Paul Graham of Y-Combinator summed up the issue extremely well in his 2006 essay, “Are Software Patents Evil?”

“The problem with Amazon’s notorious one-click patent,” he wrote, “is not that it’s a software patent but that it’s obvious… we, as hackers, know the USPTO is letting people patent the knives and forks of our world. The problem is, the USPTO are not hackers. They’re probably good at judging new inventions for casting steel or grinding lenses but they don’t understand software yet.”

The rest of Graham’s essay is dedicated to discussing the growing problem of patent trolls and why he still advises start-ups to apply for patents. It’s down to defence, rather than attack. As a start-up nears a new funding round or acquisition, the patent vultures begin to circle.

Since Graham coalesced his thoughts on software patents over six years ago, the situation has only got worse. A more recent essay by Instapaper creator Marco Arment discussed how dreadful the situation now is for small developers: “Invalid patents aren’t just funny government slip-ups… since the economics of civil lawsuits, especially patent lawsuits, prevent most cases against small defendants from ever getting near a court, the potential cost to society of issuing an invalid patent is massive.

“If someone threatens your small business with a patent lawsuit, it doesn’t matter whether the patent is valid. Because for you to prove that it’s invalid would take far more time and money than you probably have. The only sensible course of action… is to settle with the patent-holder as quickly as possible for whatever amount of money they demand.

“In practice, therefore, an issued patent is a valid patent as long as the patent-holder doesn’t try to sue anyone too large. And even the largest corporations usually settle.”

But where Microsoft can throw a patent troll a wad of cash to make them go away, many small developers and entrepreneurs are sunk each year by the practice. Start-ups can find themselves stymied before they even begin.

The problems of the US patent system become the world’s problems, since they foster a culture of malicious suits and encourage the major players in technology to become ever more litigious and to acquire vast collections of defensive patents.

Our future is being mortgaged to canny lawyers and malicious litigants. Who will step in?